Gutiérrez-de-Terán Hugo, Aqvist Johan
Fundación Pública Galega de Medicina Xenómica, Santiago University Hospital, Santiago de Compostela, Spain.
Methods Mol Biol. 2012;819:305-23. doi: 10.1007/978-1-61779-465-0_20.
A broad range of computational methods exist for the estimation of ligand-protein binding affinities. In this chapter we will provide a guide to the linear interaction energy (LIE) method for binding free energy calculations, focusing on the drug design problem. The method is implemented in combination with molecular dynamics (MD) sampling of relevant conformations of the ligands and complexes under consideration. The detailed procedure for MD sampling is followed by key notes in order to properly analyze such sampling and obtain sufficiently accurate estimations of ligand-binding affinities.
存在多种用于估计配体 - 蛋白质结合亲和力的计算方法。在本章中，我们将提供一份关于用于结合自由能计算的线性相互作用能（LIE）方法的指南，重点关注药物设计问题。该方法是结合对所考虑的配体和复合物的相关构象进行分子动力学（MD）采样来实现的。MD采样的详细过程之后是关键要点，以便正确分析此类采样并获得足够准确的配体结合亲和力估计值。
